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parallel: Fixed bug #40001: --joblog and --nonall seem not to work together:
This commit is contained in:
Ole Tange
parent
c7e0bbfbb3
commit
2bbfdfec60
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@ -208,6 +208,29 @@ available for download at: http://ftp.gnu.org/gnu/parallel/
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New in this release:
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* Using GNU Parallel to roll-your-own Map Reduce!
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http://www.rankfocus.com/hello-world/
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* 平行化你的工作
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http://www.slideshare.net/drakeguan/part1-23705978
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* Best Practices for Amazon EMR
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http://media.amazonwebservices.com/AWS_Amazon_EMR_Best_Practices.pdf
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* Using GNU Parallel at HPC @ Uni.lu
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https://hpc.uni.lu/users/use_cases/
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* Scaling up with parallelization
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https://www.msi.umn.edu/sites/default/files/AdvPython_1.pdf
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* Optimizing translated file downloads
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http://www.smartling.com/blog/2013/05/20/optimizing-translated-file-downloads/
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https://identi.ca/evan/note/6yf1GzAARtyBhj__xzMvAg
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* Faster Rasters For All
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http://2013.foss4g.org/conf/programme/presentations/52/
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* Bug fixes and man page updates.
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@ -5465,8 +5465,10 @@ sub max_length {
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close $fh;
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} else {
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$cached_limit = real_max_length();
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Semaphore::mkdir_or_die($ENV{'HOME'} . "/.parallel/tmp");
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open(my $fh, ">", $len_cache) || ::die_bug("Cannot write $len_cache");
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# If $HOME is write protected: Do not fail
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mkdir($ENV{'HOME'} . "/.parallel");
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mkdir($ENV{'HOME'} . "/.parallel/tmp");
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open(my $fh, ">", $len_cache);
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print $fh $cached_limit;
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close $fh;
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}
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BIN
src/parallel.pdf
BIN
src/parallel.pdf
Binary file not shown.
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@ -3542,23 +3542,32 @@ The error message you get (if any).
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=item *
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The output of B<parallel --version>. If you are not running the latest
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released version you should specify why you believe the problem is not
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fixed in that version.
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The complete output of B<parallel --version>. If you are not running
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the latest released version you should specify why you believe the
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problem is not fixed in that version.
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=item *
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A complete example that others can run that shows the problem. This
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should preferably be small and simple. A combination of B<yes>, B<seq>,
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B<cat>, B<echo>, and B<sleep> can reproduce most errors. If your
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example requires large files, see if you can make them by something
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like B<seq 1000000> > B<file> or B<yes | head -n 10000000> > B<file>.
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should preferably be small and simple. A combination of B<yes>,
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B<seq>, B<cat>, B<echo>, and B<sleep> can reproduce most errors. If
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your example requires large files, see if you can make them by
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something like B<seq 1000000> > B<file> or B<yes | head -n 10000000> >
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B<file>. If your example requires remote execution, see if you can
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use B<localhost>.
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=item *
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The output of your example. If your problem is not easily reproduced
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by others, the output might help them figure out the problem.
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=item *
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Whether you have watched the intro videos
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(http://www.youtube.com/playlist?list=PL284C9FF2488BC6D1), walked
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through the tutorial (man parallel_tutorial), and read the EXAMPLE
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section in the man page (man parallel - search for EXAMPLE:).
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=back
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If you suspect the error is dependent on your environment or
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@ -456,8 +456,8 @@ Set the end of file string to eof-str. If the end of file string
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occurs as a line of input, the rest of the input is ignored. If
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neither @strong{-E} nor @strong{-e} is used, no end of file string is used.
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@item @strong{--delay} @emph{secs} (alpha testing)
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@anchor{@strong{--delay} @emph{secs} (alpha testing)}
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@item @strong{--delay} @emph{secs} (beta testing)
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@anchor{@strong{--delay} @emph{secs} (beta testing)}
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Delay starting next job @emph{secs} seconds. GNU @strong{parallel} will pause
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@emph{secs} seconds after starting each job. @emph{secs} can be less than 1
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@ -483,8 +483,8 @@ because it is POSIX compliant for @strong{xargs} while this option is not.
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If @emph{eof-str} is omitted, there is no end of file string. If neither
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@strong{-E} nor @strong{-e} is used, no end of file string is used.
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@item @strong{--env} @emph{var} (alpha testing)
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@anchor{@strong{--env} @emph{var} (alpha testing)}
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@item @strong{--env} @emph{var} (beta testing)
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@anchor{@strong{--env} @emph{var} (beta testing)}
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Copy environment variable @emph{var}. This will copy @emph{var} to the
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environment that the command is run in. This is especially useful for
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@ -516,8 +516,8 @@ See also @strong{--bg}, @strong{man sem}.
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Implies @strong{--semaphore}.
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@item @strong{--filter-hosts} (alpha testing)
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@anchor{@strong{--filter-hosts} (alpha testing)}
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@item @strong{--filter-hosts} (beta testing)
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@anchor{@strong{--filter-hosts} (beta testing)}
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Remove down hosts. For each remote host: check that login through ssh
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works. If not: do not use this host.
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@ -582,8 +582,8 @@ status will be the exit status from the failing job.
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@end table
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@item @strong{--header} @emph{regexp} (alpha testing)
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@anchor{@strong{--header} @emph{regexp} (alpha testing)}
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@item @strong{--header} @emph{regexp} (beta testing)
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@anchor{@strong{--header} @emph{regexp} (beta testing)}
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Use regexp as header. For normal usage the matched header (typically
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the first line: @strong{--header '.*\n'}) will be split using @strong{--colsep}
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@ -757,8 +757,8 @@ standard specifies @strong{-L} instead.
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Implies @strong{-X} unless @strong{-m}, @strong{--xargs}, or @strong{--pipe} is set.
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@item @strong{--line-buffer} (alpha testing)
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@anchor{@strong{--line-buffer} (alpha testing)}
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@item @strong{--line-buffer} (beta testing)
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@anchor{@strong{--line-buffer} (beta testing)}
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Buffer output on line basis. @strong{--group} will keep the output together
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for a whole job. @strong{--ungroup} allows output to mixup with half a line
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@ -827,8 +827,8 @@ GNU @strong{parallel} is less than @emph{version} the exit code is
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This is useful for scripts that depend on features only available from
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a certain version of GNU @strong{parallel}.
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@item @strong{--nonall}
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@anchor{@strong{--nonall}}
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@item @strong{--nonall} (alpha testing)
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@anchor{@strong{--nonall} (alpha testing)}
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@strong{--onall} with no arguments. Run the command on all computers given
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with @strong{--sshlogin} but take no arguments. GNU @strong{parallel} will log
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@ -838,8 +838,8 @@ computer. @strong{-j} adjusts how many computers to log into in parallel.
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This is useful for running the same command (e.g. uptime) on a list of
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servers.
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@item @strong{--onall}
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@anchor{@strong{--onall}}
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@item @strong{--onall} (alpha testing)
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@anchor{@strong{--onall} (alpha testing)}
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Run all the jobs on all computers given with @strong{--sshlogin}. GNU
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@strong{parallel} will log into @strong{--jobs} number of computers in parallel
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@ -862,11 +862,11 @@ all the output from one server will be grouped together.
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Instead of printing the output to stdout (standard output) the output
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of each job is saved in a file and the filename is then printed.
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@item @strong{--pipe} (alpha testing)
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@anchor{@strong{--pipe} (alpha testing)}
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@item @strong{--pipe} (beta testing)
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@anchor{@strong{--pipe} (beta testing)}
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@item @strong{--spreadstdin} (alpha testing)
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@anchor{@strong{--spreadstdin} (alpha testing)}
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@item @strong{--spreadstdin} (beta testing)
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@anchor{@strong{--spreadstdin} (beta testing)}
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Spread input to jobs on stdin (standard input). Read a block of data
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from stdin (standard input) and give one block of data as input to one
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@ -1029,8 +1029,8 @@ If the stdin (standard input) only contains whitespace, do not run the command.
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If used with @strong{--pipe} this is slow.
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@item @strong{--record-env} (alpha testing)
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@anchor{@strong{--record-env} (alpha testing)}
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@item @strong{--record-env} (beta testing)
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@anchor{@strong{--record-env} (beta testing)}
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Record current environment variables in ~/.parallel/ignored_vars. This
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is useful before using @strong{--env _}.
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@ -1080,11 +1080,11 @@ it to the command.
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Only used with @strong{--pipe}.
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@item @strong{--results} @emph{prefix} (alpha testing)
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@anchor{@strong{--results} @emph{prefix} (alpha testing)}
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@item @strong{--results} @emph{prefix} (beta testing)
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@anchor{@strong{--results} @emph{prefix} (beta testing)}
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@item @strong{--res} @emph{prefix} (alpha testing)
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@anchor{@strong{--res} @emph{prefix} (alpha testing)}
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@item @strong{--res} @emph{prefix} (beta testing)
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@anchor{@strong{--res} @emph{prefix} (beta testing)}
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Save the output into files. The files will be stored in a directory tree
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rooted at @emph{prefix}. Within this directory tree, each command will result
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@ -1206,11 +1206,11 @@ times:
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@strong{--return} is ignored when used with @strong{--sshlogin :} or when not used
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with @strong{--sshlogin}.
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@item @strong{--round-robin} (alpha testing)
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@anchor{@strong{--round-robin} (alpha testing)}
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@item @strong{--round-robin} (beta testing)
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@anchor{@strong{--round-robin} (beta testing)}
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@item @strong{--round} (alpha testing)
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@anchor{@strong{--round} (alpha testing)}
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@item @strong{--round} (beta testing)
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@anchor{@strong{--round} (beta testing)}
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Normally @strong{--pipe} will give a single block to each instance of the
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command. With @strong{--round-robin} all blocks will at random be written to
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@ -1419,11 +1419,11 @@ The remote host must have GNU @strong{parallel} installed.
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@strong{--sshlogin} is often used with @strong{--transfer}, @strong{--return},
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@strong{--cleanup}, and @strong{--trc}.
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@item @strong{--sshloginfile} @emph{filename} (alpha testing)
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@anchor{@strong{--sshloginfile} @emph{filename} (alpha testing)}
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@item @strong{--sshloginfile} @emph{filename} (beta testing)
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@anchor{@strong{--sshloginfile} @emph{filename} (beta testing)}
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@item @strong{--slf} @emph{filename} (alpha testing)
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@anchor{@strong{--slf} @emph{filename} (alpha testing)}
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@item @strong{--slf} @emph{filename} (beta testing)
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@anchor{@strong{--slf} @emph{filename} (beta testing)}
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File with sshlogins. The file consists of sshlogins on separate
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lines. Empty lines and lines starting with '#' are ignored. Example:
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@ -1516,8 +1516,8 @@ into temporary files in /tmp. By setting @strong{--tmpdir} you can use a
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different dir for the files. Setting @strong{--tmpdir} is equivalent to
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setting $TMPDIR.
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@item @strong{--timeout} @emph{val} (alpha testing)
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@anchor{@strong{--timeout} @emph{val} (alpha testing)}
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@item @strong{--timeout} @emph{val} (beta testing)
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@anchor{@strong{--timeout} @emph{val} (beta testing)}
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Time out for command. If the command runs for longer than @emph{val}
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seconds it will get killed with SIGTERM, followed by SIGTERM 200 ms
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@ -1673,11 +1673,11 @@ Use @strong{-v} @strong{-v} to print the wrapping ssh command when running remot
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Print the version GNU @strong{parallel} and exit.
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@item @strong{--workdir} @emph{mydir} (alpha testing)
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@anchor{@strong{--workdir} @emph{mydir} (alpha testing)}
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@item @strong{--workdir} @emph{mydir} (beta testing)
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@anchor{@strong{--workdir} @emph{mydir} (beta testing)}
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@item @strong{--wd} @emph{mydir} (alpha testing)
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@anchor{@strong{--wd} @emph{mydir} (alpha testing)}
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@item @strong{--wd} @emph{mydir} (beta testing)
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@anchor{@strong{--wd} @emph{mydir} (beta testing)}
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Files transferred using @strong{--transfer} and @strong{--return} will be relative
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to @emph{mydir} on remote computers, and the command will be executed in
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@ -3786,19 +3786,26 @@ Your bug report should always include:
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@itemize
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@item The error message you get (if any).
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@item The output of @strong{parallel --version}. If you are not running the latest
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released version you should specify why you believe the problem is not
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fixed in that version.
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@item The complete output of @strong{parallel --version}. If you are not running
|
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the latest released version you should specify why you believe the
|
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problem is not fixed in that version.
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@item A complete example that others can run that shows the problem. This
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should preferably be small and simple. A combination of @strong{yes}, @strong{seq},
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@strong{cat}, @strong{echo}, and @strong{sleep} can reproduce most errors. If your
|
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example requires large files, see if you can make them by something
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like @strong{seq 1000000} > @strong{file} or @strong{yes | head -n 10000000} > @strong{file}.
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should preferably be small and simple. A combination of @strong{yes},
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@strong{seq}, @strong{cat}, @strong{echo}, and @strong{sleep} can reproduce most errors. If
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your example requires large files, see if you can make them by
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something like @strong{seq 1000000} > @strong{file} or @strong{yes | head -n 10000000} >
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@strong{file}. If your example requires remote execution, see if you can
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use @strong{localhost}.
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@item The output of your example. If your problem is not easily reproduced
|
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by others, the output might help them figure out the problem.
|
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|
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@item Whether you have watched the intro videos
|
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(http://www.youtube.com/playlist?list=PL284C9FF2488BC6D1), walked
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through the tutorial (man parallel_tutorial), and read the EXAMPLE
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section in the man page (man parallel - search for EXAMPLE:).
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@end itemize
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If you suspect the error is dependent on your environment or
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@ -124,7 +124,7 @@
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.\" ========================================================================
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.\"
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.IX Title "PARALLEL_TUTORIAL 1"
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.TH PARALLEL_TUTORIAL 1 "2013-09-18" "20130922" "parallel"
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.TH PARALLEL_TUTORIAL 1 "2013-09-28" "20130922" "parallel"
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.\" For nroff, turn off justification. Always turn off hyphenation; it makes
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.\" way too many mistakes in technical documents.
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.if n .ad l
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@ -465,7 +465,8 @@ Output (the order may be different):
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The command can be a script, a binary or a Bash function if the function is
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exported using 'export \-f':
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.PP
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.Vb 5
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.Vb 6
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\& # Only works in Bash and only if $SHELL=.../bash
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\& my_func() {
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\& echo in my_func $1
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\& }
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@ -1516,7 +1517,7 @@ Output:
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\& tried 0
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.Ve
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.PP
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Note how job 1 and 2 was tried 3 times, but 0 was not retried because it had exit code 0.
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Note how job 1 and 2 were tried 3 times, but 0 was not retried because it had exit code 0.
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.SS "Limiting the ressources"
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.IX Subsection "Limiting the ressources"
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To avoid overloading systems \s-1GNU\s0 Parallel can look at the system load
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@ -1858,9 +1859,10 @@ Output:
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\& foo bar baz
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.Ve
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.PP
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This works for functions too:
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This works for functions too if your shell is Bash:
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.PP
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.Vb 5
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.Vb 6
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\& # This only works in Bash
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\& my_func() {
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\& echo in my_func $1
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\& }
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@ -1892,7 +1894,8 @@ Output:
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Now all new variables and functions defined will be copied when using
|
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\&\-\-env _:
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.PP
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.Vb 6
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.Vb 7
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\& # The function is only copied if using Bash
|
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\& my_func2() {
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\& echo in my_func2 $VAR $1
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\& }
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@ -1900,12 +1903,13 @@ Now all new variables and functions defined will be copied when using
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\& VAR=foo
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\& export VAR
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\&
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\& parallel \-\-env _ \-S $SERVER1 my_func2 ::: bar
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\& parallel \-\-env _ \-S $SERVER1 \*(Aqecho $VAR; my_func2\*(Aq ::: bar
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.Ve
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.PP
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Output:
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.PP
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.Vb 1
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.Vb 2
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\& foo
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\& in my_func2 foo bar
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.Ve
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.SS "Showing what is actually run"
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|
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@ -374,6 +374,7 @@ treated as commands:</p>
|
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<p>The command can be a script, a binary or a Bash function if the function is
|
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exported using 'export -f':</p>
|
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<pre>
|
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# Only works in Bash and only if $SHELL=.../bash
|
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my_func() {
|
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echo in my_func $1
|
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}
|
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|
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@ -1051,7 +1052,7 @@ command fails for unkown reasons now and then.</p>
|
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tried 1
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tried 2
|
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tried 0</pre>
|
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<p>Note how job 1 and 2 was tried 3 times, but 0 was not retried because it had exit code 0.</p>
|
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<p>Note how job 1 and 2 were tried 3 times, but 0 was not retried because it had exit code 0.</p>
|
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<p>
|
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</p>
|
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<h2><a name="limiting_the_ressources">Limiting the ressources</a></h2>
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|
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@ -1274,8 +1275,9 @@ remote system.</p>
|
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<p>Output:</p>
|
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<pre>
|
||||
foo bar baz</pre>
|
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<p>This works for functions too:</p>
|
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<p>This works for functions too if your shell is Bash:</p>
|
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<pre>
|
||||
# This only works in Bash
|
||||
my_func() {
|
||||
echo in my_func $1
|
||||
}
|
||||
|
|
@ -1296,6 +1298,7 @@ remote system. It just need to record which ones to ignore in
|
|||
<p>Now all new variables and functions defined will be copied when using
|
||||
--env _:</p>
|
||||
<pre>
|
||||
# The function is only copied if using Bash
|
||||
my_func2() {
|
||||
echo in my_func2 $VAR $1
|
||||
}
|
||||
|
|
@ -1303,9 +1306,10 @@ remote system. It just need to record which ones to ignore in
|
|||
VAR=foo
|
||||
export VAR</pre>
|
||||
<pre>
|
||||
parallel --env _ -S $SERVER1 my_func2 ::: bar</pre>
|
||||
parallel --env _ -S $SERVER1 'echo $VAR; my_func2' ::: bar</pre>
|
||||
<p>Output:</p>
|
||||
<pre>
|
||||
foo
|
||||
in my_func2 foo bar</pre>
|
||||
<p>
|
||||
</p>
|
||||
|
|
|
|||
Binary file not shown.
|
|
@ -285,6 +285,7 @@ Output (the order may be different):
|
|||
The command can be a script, a binary or a Bash function if the function is
|
||||
exported using 'export -f':
|
||||
|
||||
# Only works in Bash and only if $SHELL=.../bash
|
||||
my_func() {
|
||||
echo in my_func $1
|
||||
}
|
||||
|
|
@ -1089,7 +1090,7 @@ Output:
|
|||
tried 2
|
||||
tried 0
|
||||
|
||||
Note how job 1 and 2 was tried 3 times, but 0 was not retried because it had exit code 0.
|
||||
Note how job 1 and 2 were tried 3 times, but 0 was not retried because it had exit code 0.
|
||||
|
||||
=head2 Limiting the ressources
|
||||
|
||||
|
|
@ -1358,8 +1359,9 @@ Output:
|
|||
|
||||
foo bar baz
|
||||
|
||||
This works for functions too:
|
||||
This works for functions too if your shell is Bash:
|
||||
|
||||
# This only works in Bash
|
||||
my_func() {
|
||||
echo in my_func $1
|
||||
}
|
||||
|
|
@ -1384,6 +1386,7 @@ Output:
|
|||
Now all new variables and functions defined will be copied when using
|
||||
--env _:
|
||||
|
||||
# The function is only copied if using Bash
|
||||
my_func2() {
|
||||
echo in my_func2 $VAR $1
|
||||
}
|
||||
|
|
@ -1391,10 +1394,11 @@ Now all new variables and functions defined will be copied when using
|
|||
VAR=foo
|
||||
export VAR
|
||||
|
||||
parallel --env _ -S $SERVER1 my_func2 ::: bar
|
||||
parallel --env _ -S $SERVER1 'echo $VAR; my_func2' ::: bar
|
||||
|
||||
Output:
|
||||
|
||||
foo
|
||||
in my_func2 foo bar
|
||||
|
||||
=head2 Showing what is actually run
|
||||
|
|
|
|||
|
|
@ -12,4 +12,9 @@ echo '### --env _ with explicit mentioning of normally ignored var $DISPLAY'
|
|||
echo '### --filter-hosts --slf <()'
|
||||
parallel --nonall --filter-hosts --slf <(echo localhost) echo OK
|
||||
|
||||
echo '### bug #40002: --files and --nonall seem not to work together:'
|
||||
parallel --files --nonall -S localhost true | tee >(parallel rm) | wc -l
|
||||
|
||||
echo '### bug #40001: --joblog and --nonall seem not to work together:'
|
||||
parallel --joblog - --nonall -S lo,localhost true | wc -l
|
||||
EOF
|
||||
|
|
|
|||
|
|
@ -9,6 +9,10 @@ Block_end
|
|||
### --env _
|
||||
DISPLAY: Undefined variable.
|
||||
### --env _ with explicit mentioning of normally ignored var $DISPLAY
|
||||
OK FUBAR :0 test
|
||||
OK FUBAR :0.0 test
|
||||
### --filter-hosts --slf <()
|
||||
OK
|
||||
### bug #40002: --files and --nonall seem not to work together:
|
||||
1
|
||||
### bug #40001: --joblog and --nonall seem not to work together:
|
||||
3
|
||||
|
|
|
|||
Loading…
Reference in a new issue